Reorder organs for plotting
expr.var.rank.common <- expr.var.common %>%
dplyr::inner_join(expr.rank.first, by="GeneID")
if ("Sex" %in% colnames(filtered.samples$metadata)) {
levels.order <-
c("brain","eye","intestine","liver",
"heart","muscle","gills","pectoral_fin",
"ovary","testis")
} else {
levels.order <-
c("brain","eye","intestine","liver",
"heart","muscle","gills","pectoral_fin","gonads")
}
# Exclude missing conditions from factor levels
levels.exclude <- setdiff(levels.order, levels(as.factor(expr.var.rank.common$Tissue)))
# Reorder levels for plotting
expr.var.rank.common$Tissue <-
factor(expr.var.rank.common$Tissue, levels=levels.order, exclude=levels.exclude)
Density plots
Variability rank vs. mean expression
density_plot_variability_vs_mean(expr.var.rank.common, title=params$species.name)

Mean expression vs. tau
density_plot_mean_vs_tau(expr.var.rank.common, title=params$species.name)

Residual variation vs. tau
density_plot_resid_var_vs_tau(expr.var.rank.common, title=params$species.name)

Variability rank vs. tau
density_plot_variability_vs_tau(expr.var.rank.common, title=params$species.name)

Boxplots by tau quantiles
Split by tau quantiles
tau.with.var.quantiles <- quantile(tau.with.var)
expr.var.rank.common$Quantile <-
apply(expr.var.rank.common, MARGIN=1, function(r) {
if (r[["tau"]] <= tau.with.var.quantiles["25%"]) { "Q1" }
else if (r[["tau"]] <= tau.with.var.quantiles["50%"]) { "Q2" }
else if (r[["tau"]] <= tau.with.var.quantiles["75%"]) { "Q3" }
else { "Q4" }
})
print(tau.with.var.quantiles)
## 0% 25% 50% 75% 100%
## 0.03910663 0.18645619 0.26382625 0.37485886 0.80821801
Mean expression
boxplot_mean_by_tau_quantiles(expr.var.rank.common, title=species.name)

Residual variation
boxplot_resid_var_by_tau_quantiles(expr.var.rank.common, title=species.name)
